Closed bioinfo-dirty-jobs closed 6 years ago
Here the error:
type == 'gene_expression' & + analysis.workflow_type == 'HTSeq - Counts') > manifest_df = qfiles %>% manifest() Error: lexical error: invalid char in json text. <?xml version="1.0" encoding="U (right here) ------^ sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_2.2.1 knitr_1.20 GenomicDataCommons_1.2.0 [4] magrittr_1.5 loaded via a namespace (and not attached): [1] Rcpp_0.12.17 pillar_1.2.3 compiler_3.4.4 [4] BiocInstaller_1.28.0 GenomeInfoDb_1.14.0 plyr_1.8.4 [7] XVector_0.18.0 bitops_1.0-6 tools_3.4.4 [10] zlibbioc_1.24.0 jsonlite_1.5 tibble_1.4.2 [13] gtable_0.2.0 pkgconfig_2.0.1 rlang_0.2.0 [16] rstudioapi_0.7 curl_3.2 yaml_2.1.19 [19] parallel_3.4.4 GenomeInfoDbData_1.0.0 httr_1.3.1 [22] xml2_1.2.0 S4Vectors_0.16.0 IRanges_2.12.0 [25] hms_0.4.2 stats4_3.4.4 grid_3.4.4 [28] data.table_1.11.4 R6_2.2.2 readr_1.1.1 [31] scales_0.5.0 BiocGenerics_0.24.0 GenomicRanges_1.30.3 [34] colorspace_1.3-2 labeling_0.3 utf8_1.1.4 [37] RCurl_1.95-4.10 lazyeval_0.2.1 munsell_0.4.3 [40] crayon_1.3.4
Upgrading to version 1.4.1 (the current release version) should fix the issue. A change on the NCI GDC server causes this error, so an upgrade is required. Sorry about the inconvenience.
Here the error: